Charakterisierung der DNA-Methylierung geprägter Gene im Kontext physiologischer und gestörter Entwicklung und somatischer Differenzierung

Die Expression von Genen in Abhängigkeit von der elterlichen Herkunft des Allels wird als Imprinting (“Prägung“) bezeichnet. Diese Eltern-spezifische Expression wird u.a. durch die Allel-spezifische DNA-Methylierung differenziell methylierter Regionen (DMRs) reguliert. Dabei liegt eine DMR in der Regel auf einem der beiden elterlichen Allele methyliert und auf dem anderen Allel unmethyliert vor. Da viele geprägte Gene in Wachstums- und Differenzierungsprozesse eingebunden sind, ist die korrekte Regulation der Expression geprägter Gene wichtig für die physiologische Entwicklung. Eine gestörte DNA-Methylierung von DMRs kann die aberrante Expression elterlich geprägter Gene bewirken. Konstitutionelle Störungen der elterlichen Prägung sind sowohl mit klassischen Imprintingsyndromen als auch mit Multi-Locus Methylierungsdefekten (MLMD) assoziiert. DNA-Methylierungsstörungen geprägter Gene werden aber auch bei benignen und malignen somatischen Erkrankungen beschrieben und können zu deren Krankheitsentstehung und Progression beitragen. Ausgangspunkt für die vorliegende Arbeit waren, bis auf die IG-DMR auf Chromosom 14q32.2, sämtliche 34 somatisch und 20 Plazenta-spezifisch geprägten DMRs des Menschen. Da diese DMRs z.T. erst jüngst beschrieben wurden, sind zu vielen keine systematischen DNA-Methylierungsdaten zur physiologischen Entwicklung oder zu pathologischen Prozessen publiziert. Deshalb war das Ziel dieser Arbeit, die physiologische DNA-Methylierung dieser geprägten DMRs in pränatalen und postnatalen Normalgeweben auch unter Berücksichtigung des Einflusses der Gewebefixierung zu charakterisieren. Weiterhin sollte die DNA-Methylierung dieser DMRs im Kontext benigner und maligner somatischer Erkrankungen, konstitutioneller Störungen und in Patienten-spezifischen induzierten pluripotenten Stammzellen (iPSZ) analysiert werden...The term parental imprinting describes the expression of genes dependend of the parental origin of the alleles. This parental-specific expression is regulated amongst others by allele-specific DNA-methylation of differentially methylated regions (DMRs). In general, the DMR on one of the two parental alleles is methylated while the other is unmethylated. Due to the involvement of imprinted genes in growth and differentiation processes the accurate regulation of imprinted gene expression is important for the physiological development. A disturbed DNA-methylation at a DMR can cause the aberrant expression of parent-specific imprinted genes. Constitutional disturbances of the parental imprinting are associated with classical imprinting disorders as well as with multi locus methylation defects (MLMD). Moreover, aberrant DNA-methylation of imprinted genes has also been described in benign and malignant somatic diseases and may contribute to their development and progression. All 34 somatic, except for the somatic IG-DMR on chromosome 14q32.2, and 20 placental-specific human imprinted genes were analysed in this study. Since these DMRs have been described just recently DNA-methylation data concerning the physiological development or regarding pathological processes have yet not been published. Therefore, the aim of this study was to characterize the physiological DNA-methylation of these imprinted DMRs in prenatal and postnatal normal tissues. Moreover, the influence of tissue fixation on DNA-methylation should be studied. Furthermore, the DNA-methylation of these DMRs should be analysed in context of benign and malignant somatic diseases, constitutional disorders and in patient-specific induced pluripotent stem cells (iPSC)..

Vitamin B12 in Leber hereditary optic neuropathy mutation carriers: a prospective cohort study

Background Leber hereditary optic neuropathy (LHON) is the most common mitochondrial disorder, frequently resulting in acute or subacute severe bilateral central vision loss. Vitamin B12 deficiency is also a known cause of optic neuropathy through mitochondrial dysfunction. Here we evaluated the prevalence and clinical significance of vitamin B12 deficiency in a large cohort of LHON patients and asymptomatic mutation carriers from a tertiary referral center. Methods From the Munich LHON prospective cohort study, participants included all LHON patients and asymptomatic LHON mutation carriers, who were recruited between February 2014 and March 2020 and consented to participate. Neurological, general, and ophthalmological examinations were regularly performed, as were laboratory tests. Vitamin B12 deficiency was diagnosed if serum vitamin B12 was below 201 pg/mL, or if 201–339 pg/mL plus low serum holotranscobalamin or elevated serum methylmalonic acid or elevated total plasma homocysteine. Results We analyzed 244 subjects, including 147 symptomatic LHON patients (74% males) and 97 asymptomatic mutation carriers (31% males). Median age at study baseline was 34 years (range 5–82 years). The prevalence of vitamin B12 deficiency was higher for LHON mutation carriers than for the general population in all age categories. This was statistically significant for the LHON mutation carriers under 65 years (21% vs. 5–7%, p = 0.002). While vitamin B12 deficiency prevalence was not statistically different between LHON patients and asymptomatic mutation carriers, its clinical correlates, e.g., macrocytosis and polyneuropathy, were more frequent in the subgroup of LHON patients. Excessive alcohol consumption was a significant predictor of vitamin B12 deficiency (p < 0.05). Conclusions The high prevalence of vitamin B12 deficiency in LHON mutation carriers, both asymptomatic mutation carriers and LHON patients, highlights the need for regular vitamin B12 screening in this population, in order to ensure early treatment, aiming for better outcomes. Our study is not conclusive regarding vitamin B12 deficiency as determinant for disease conversion in LHON, and further research is warranted to disentangle the role of vitamin B12 in the pathophysiology and prognosis of LHON

Genetic‐guided pharmacotherapy for coronary artery disease: a systematic and critical review of economic evaluations

Background: Genetic‐guided pharmacotherapy (PGx) is not recommended in clinical guidelines for coronary artery disease (CAD). We aimed to examine the extent and quality of evidence from economic evaluations of PGx in CAD and to identify variables influential in changing conclusions on cost‐effectiveness. Methods and Results: From systematic searches across 6 databases, 2 independent reviewers screened, included, and rated the methodological quality of economic evaluations of PGx testing to guide pharmacotherapy for patients with CAD. Of 35 economic evaluations included, most were model‐based cost‐utility analyses alone, or alongside cost‐effectiveness analyses of PGx testing to stratify patients into antiplatelets (25/35), statins (2/35), pain killers (1/35), or angiotensin‐converting enzyme inhibitors (1/35) to predict CAD risk (8/35) or to determine the coumadin doses (1/35). To stratify patients into antiplatelets (96/151 comparisons with complete findings of PGx versus non‐PGx), PGx was more effective and more costly than non‐PGx clopidogrel (28/43) but less costly than non‐PGx prasugrel (10/15) and less costly and less effective than non‐PGx ticagrelor (22/25). To predict CAD risk (51/151 comparisons), PGx using genetic risk scores was more effective and less costly than clinical risk score (13/17) but more costly than no risk score (16/19) or no treatment (9/9). The remaining comparisons were too few to observe any trend. Mortality risk was the most common variable (47/294) changing conclusions. Conclusions: Economic evaluations to date found PGx to stratify patients with CAD into antiplatelets or to predict CAD risk to be cost‐effective, but findings varied based on the non‐PGx comparators, underscoring the importance of considering local practice in deciding whether to adopt PGx

DNA-Methylation Profiling of Fetal Tissues Reveals Marked Epigenetic Differences between Chorionic and Amniotic Samples

Epigenetic mechanisms including DNA methylation are supposed to play a key role in fetal development. Here we have investigated fetal DNA-methylation levels of 27,578 CpG loci in 47 chorionic villi (CVS) and 16 amniotic cell (AC) samples. Methylation levels differed significantly between karyotypically normal AC and CVS for 2,014 genes. AC showed more extreme DNA-methylation levels of these genes than CVS and the differentially methylated genes are significantly enriched for processes characteristic for the different cell types sampled. Furthermore, we identified 404 genes differentially methylated in CVS with trisomy 21. These genes were significantly enriched for high CG dinucleotid (CpG) content and developmental processes associated with Down syndrome. Our study points to major tissue-specific differences of fetal DNA-methylation and gives rise to the hypothesis that part of the Down syndrome phenotype is epigenetically programmed in the first trimester of pregnancy

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite, genome and transcriptome sequencing in 13 IG-MYC translocation-positive Burkitt lymphoma, nine BCL2 translocation-positive follicular lymphoma and four normal germinal center B cell samples. Comparison of Burkitt and follicular lymphoma samples showed differential methylation of intragenic regions that strongly correlated with expression of associated genes, for example, genes active in germinal center dark-zone and light-zone B cells. Integrative pathway analyses of regions differentially methylated in Burkitt and follicular lymphomas implicated DNA methylation as cooperating with somatic mutation of sphingosine phosphate signaling, as well as the TCF3-ID3 and SWI/SNF complexes, in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B cell pathways deregulated differentially in Burkitt lymphoma and other germinal center B cell lymphomas

Maternal variants in NLRP and other maternal effect proteins are associated with multilocus imprinting disturbance in offspring

Background: Genomic imprinting results from the resistance of germline epigenetic marks to reprogramming in the early embryo for a small number of mammalian genes. Genetic, epigenetic or environmental insults that prevent imprints from evading reprogramming may result in imprinting disorders, which impact growth, development, behaviour and metabolism. We aimed to identify genetic defects causing imprinting disorders, by whole-exome sequencing in families with one or more members affected by multi-locus imprinting disturbance. Methods: Whole-exome sequencing was performed in 38 pedigrees where probands had multi-locus imprinting disturbance, in five of whom, maternal variants in NLRP5 have previously been found. Results: We now report 15 further pedigrees in which offspring had disturbance of imprinting, while their mothers had rare, predicted-deleterious variants in maternal-effect genes, including NLRP2, NLRP7 and PADI6. As well as clinical features of well-recognised imprinting disorders, some offspring had additional features including developmental delay, behavioural problems and discordant monozygotic twinning, while some mothers had reproductive problems including pregnancy loss. Conclusion: The identification of 20 putative maternal-effect variants in 38 families affected by multi-locus imprinting disorders adds to the evidence that maternal genetic factors affect oocyte fitness and thus offspring development. Testing for maternal-effect genetic variants should be considered in families affected by atypical imprinting disorders.<br/

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Early adopters of electric vehicles in Germany unveiled

The socioeconomic characteristics of early adopters of electric vehicles (EVs) differ from those of buyers of conventional vehicles, as do their attitudes towards new technologies, their mobility, and their awareness of ecological issues. They are found to have a higher average income, a higher level of education and more cars at their disposal per household. However, most of the existing studies are based on small samples, or used stated preference surveys which attempted to describe potential purchasers of EVs. Furthermore, when it comes to the kind of EV, most of the studies analyse the adoption of battery electric vehicles (BEVs) only, with just a few looking at the adoption of plug-in hybrid electric vehicles (PHEVs). An analysis of representative data collected from more than 3,000 owners of BEVs and PHEVs in Germany partially confirms the findings mentioned, but finds that aspects such as socioeconomic characteristics and their attitudes vary greatly among EV users. First the paper gives an overview of the socioeconomics of EV drivers in Germany, and key facts about their driving and charging behaviour. Subsequently, the main factors motivating people to buy an EV are identified and analysed for owners of BEVs and PHEVs. This is complemented by an analysis of general attitudes of EV owners towards factors such as the image of EVs, environmental awareness and mode choice. To conclude, the willingness to pay for technologies such as fast-charging, inductive charging and battery size selection is analysed